- Company registration with BRS and a KRA PIN
- eTIMS set-up from your first sale
- Books in Zoho Books from day one
- Turnover tax or VAT: which applies to you
SMEs and growing businesses
Accounting, tax and compliance for SMEs in Kenya
FNJ & Associates is an ICPAK-registered CPA firm and authorized Zoho partner in Nairobi that keeps small and growing businesses in Kenya compliant and ready to grow. Our accounting services for SMEs in Kenya cover bookkeeping in Zoho Books, tax and payroll filed on time through iTax and eTIMS, audits, and getting you ready for lenders, tenders and investors.
ICPAK-registered CPA firmAuthorized Zoho partnereTIMS-ready bookkeepingNairobi, serving East Africa
Who we help
Support for every stage of your business
Kenya's tax and compliance rules change as a business grows: a new threshold, a first employee or a bank loan. We set up what you need for the stage you are at.
- VAT registration once taxable sales reach KES 5 million a year
- Payroll and statutory deductions for your first employees
- Withholding tax on supplier payments
- Monthly management accounts
- Audited financial statements
- Business plans and financial projections
- A clean tax record and a valid tax compliance certificate
- Internal controls a funder can rely on
Services
Accounting services for SMEs in Kenya
Bookkeeping and Zoho Books
Monthly bookkeeping, bank and M-Pesa reconciliations, and Zoho Books set-up, migration and training.
Zoho Books with FNJTax and eTIMS
VAT, turnover tax, withholding tax and income tax returns, eTIMS set-up, and help with KRA assessments and the 2026 amnesty.
Tax servicesPayroll
Monthly payroll with PAYE, SHIF, NSSF, Housing Levy and NITA calculated and remitted on time, and payslips for your team.
Get payroll done for youAudit and assurance
Statutory audits and audited accounts for banks, investors, tenders and KRA, prepared under IFRS for SMEs where it applies.
Audit and assuranceCompany and regulatory filings
BRS annual returns, beneficial ownership filings, ODPC data protection registration and county business permits.
Request a proposalFunding and tenders
Business plans, financial projections and lender-ready accounts, tax compliance certificates and AGPO registration.
Request a proposalCash flow and CFO support
Cash-flow forecasts, budgets and part-time finance leadership for owners who need numbers they can act on.
Request a proposalControls and fraud prevention
Simple approval and payment controls, payroll and procurement checks, and fraud risk reviews sized for a small team.
Fraud risk assessmentCompliance calendar
What an SME in Kenya must file, and when
The main deadlines for a limited company or sole trader in Kenya, as of 17 October 2026. Each row links to the official source.
| Obligation | When it is due | Who it applies to | Source |
|---|---|---|---|
| Withholding tax | Within 5 working days of each payment | Businesses making qualifying payments, such as professional fees, consultancy and rent, to residents or non-residents | KRA |
| PAYE, SHIF, NSSF and NITA levy | 9th of the following month | Every employer | KRA |
| Affordable Housing Levy | 9th working day after the end of the month | Every employer: 1.5% from the employee and 1.5% from the employer | KRA |
| VAT return and payment | 20th of the following month | Businesses with taxable sales of KES 5 million or more in 12 months | KRA |
| Turnover tax | 20th of the following month | Resident businesses with turnover above KES 1 million and up to KES 25 million (1.5% of gross sales) | KRA |
| Instalment tax | 20th day of the 4th, 6th, 9th and 12th months of the accounting year | Companies expecting to owe corporate tax (30%) | KRA |
| Company income tax return | Balance of tax by the end of the 4th month after year end; return by the end of the 6th month | Companies | KRA |
| Individual income tax return | 30 June for 2025 returns; 30 April from 2027 for many individuals | Individuals, including sole traders. We confirm which deadline applies to you | KRA |
| Beneficial ownership | Register lodged within 30 days; changes within 14 days | Companies, for anyone holding 10% or more of shares or votes | BRS |
| Annual return | Every year | Companies registered with BRS | BRS |
| Tax compliance certificate | Valid for 12 months | Businesses bidding for tenders or registering for AGPO | KRA |
| ODPC registration | Renew every 2 years | Businesses that hold personal data, unless turnover is below KES 5 million and staff below 10; some sectors at any size | ODPC |
Want every deadline in one place? See our Kenya tax calendar.
What changed in 2026
Tax and payroll changes SMEs need to know
Status as of 17 October 2026. Proposals are shown as proposals, not law.
| Change | Status | What to do |
|---|---|---|
| Tax amnesty under the Finance Act 2026 | IN FORCE Penalties and interest on tax owed up to 31 Dec 2025 are waived if the principal is paid by 31 Dec 2026. Source | Check your iTax ledger now and clear old balances before the deadline. |
| eTIMS invoices for every expense | IN FORCE A one-off allowance applied to 2025 returns. From the 2026 income year, income and expenses must be backed by eTIMS invoices. Source | Ask every supplier for an eTIMS invoice and reconcile them monthly. |
| iTax checks returns against eTIMS, withholding tax and customs data | IN FORCE Since 1 Jan 2026. Source | Make sure your books, eTIMS records and returns agree before you file. |
| Tax compliance certificate needs eTIMS compliance | IN FORCE Since October 2025, alongside VAT compliance and filed returns. Source | Fix eTIMS gaps before your certificate is due for renewal. |
| New individual filing deadline | IN FORCE From 1 Jan 2027, many individuals file by 30 April instead of 30 June. Source | Plan sole trader and director returns two months earlier. |
| NSSF contribution limits (year 4) | IN FORCE From February 2026: 6% each, on pay between KES 9,000 and 108,000, up to KES 6,480 each. Litigation is ongoing. Source | Confirm your payroll uses the new limits. |
| Housing Levy enforcement | IN FORCE KRA can now recover the levy as tax, and defaulters face bank account and PIN freezes. Source | Clear any unpaid levy and remit by the 9th working day every month. |
| PAYE relief | PROPOSED A bill to cut PAYE on lower incomes is still in public participation. Source | No change yet. Keep using the current bands. |
Is your business KRA-ready?
KRA now matches what you file against eTIMS, withholding tax and customs records. A business that can tick these nine boxes is ready for a review, a tender or a loan application.
Book a KRA health check- 1KRA PIN and iTax profile up to date
- 2Onboarded to eTIMS, with every sale invoiced
- 3Every expense backed by a supplier's eTIMS invoice
- 4VAT or turnover tax filed by the 20th
- 5PAYE, SHIF, NSSF, NITA and Housing Levy remitted on time
- 6Withholding tax remitted within 5 working days
- 7Books reconciled monthly to bank and M-Pesa statements
- 8A valid tax compliance certificate
- 9Old penalties cleared under the amnesty before 31 December 2026
Payroll
What employers deduct and pay in Kenya
Five deductions, two due dates. NSSF, SHIF and the Housing Levy are deducted before PAYE is worked out. Use our PAYE calculator to see the figures for any salary.
| Deduction | Employee pays | Employer pays | Due |
|---|---|---|---|
| PAYE | Current bands from 10% to 35%, less personal relief of KES 2,400 a month | None | 9th of the following month |
| SHIF | 2.75% of gross pay, minimum KES 300 | None | 9th of the following month |
| NSSF | 6% of pay between KES 9,000 and 108,000, up to KES 6,480 | 6%, up to KES 6,480 | 9th of the following month |
| Affordable Housing Levy | 1.5% of gross pay | 1.5% of gross pay | 9th working day after month end |
| NITA levy | None | KES 50 per employee a month | 9th of the following month, with PAYE |
Rates as of 17 October 2026. Read our guide to statutory payroll deductions.
Free tools
Calculators and guides for business owners
Our work
Engagements we deliver for SMEs
Growing businesses
Monthly bookkeeping and VAT
Books closed every month, VAT and withholding tax filed, and a short report for the owner.
Moving off Excel or QuickBooks
Zoho Books set-up and migration
Opening balances, eTIMS integration, M-Pesa and bank feeds, and staff training.
Employers
Payroll and statutory remittances
Payroll processed and every deduction remitted on time, with payslips and P9 forms.
Owners and boards
Audits and KRA clean-ups
Statutory audits, amnesty clean-ups and tax compliance certificate renewals.
We do not publish client names. References from businesses in your industry are available on request.
Guides
Guides for business owners
Tax
Tax calendar in KenyaWithholding tax in KenyaeTIMS for non-VAT registered businessesCommon iTax filing errorsMonthly rental income taxFAQ
Questions business owners ask us
When does a business in Kenya have to register for VAT?
When its taxable sales reach KES 5 million or more in any 12-month period. VAT is charged at 16%, and returns and payment are due by the 20th of the following month.
What is turnover tax and who pays it?
Turnover tax is 1.5% of gross sales for resident businesses with annual turnover above KES 1 million and up to KES 25 million. It is filed and paid monthly by the 20th. It does not cover rental income, management or professional fees, or income already taxed by final withholding tax.
Does every business need to use eTIMS?
Yes. Every person in business must issue electronic tax invoices through eTIMS, whether or not they are registered for VAT. From the 2026 income year, KRA expects income and expenses in tax returns to be backed by eTIMS invoices, with exceptions such as salaries, imports, interest and bank charges.
What payroll deductions must employers make in Kenya?
PAYE, SHIF at 2.75% of gross pay, NSSF at 6% from both employee and employer on pay between KES 9,000 and 108,000, and the Affordable Housing Levy at 1.5% from each. Employers also pay the NITA levy of KES 50 per employee. All are due by the 9th of the following month, except the Housing Levy, which is due by the 9th working day.
Does my small company need an audit?
Some small private companies may be exempt from statutory audit under the Companies Act. We confirm whether yours qualifies, and whether lenders, KRA, tender boards or shareholders will still expect audited accounts.
What is the 2026 tax amnesty?
Under the Finance Act 2026, KRA waives penalties and interest on tax owed for periods up to 31 December 2025, provided the principal tax is paid by 31 December 2026. KRA applies the waiver once the principal is cleared.
What is a tax compliance certificate and how long is it valid?
It is KRA's confirmation that a business has filed its returns and paid its taxes, and it is valid for 12 months. Since October 2025 KRA also checks eTIMS and VAT compliance before issuing it. Tenders and AGPO registration usually require one.
How much does outsourced accounting cost?
It depends on how many transactions, employees and tax filings you have each month, and on whether you need an audit. We agree a fixed monthly fee in a written proposal after a short call, so you know the cost before any work starts.
Do SMEs need to register with the Data Protection Commissioner?
Most do. A business that handles personal data must register with the ODPC unless its turnover is below KES 5 million and it has fewer than 10 employees, and businesses in sectors such as health, education, hospitality, property management and financial services must register whatever their size. Registration lasts two years.
Talk to our tax and accounting team
Tell us about your business and what is due. We reply within one working day and send a proposal within 1 to 4 working days.
This page gives general information about Kenyan tax, payroll and company compliance rules as at 17 October 2026. It is not tax, legal or financial advice for your business, and rates, thresholds and deadlines can change. Our fees depend on the size of your business and the work involved, and we confirm them in a written proposal before any work starts.